FASA Games, Inc.

I'd assume that the Amaltheans/Sanctuary Aeon can see the benefit of Cybernetics to treat disability or restore facility. However how does that sit with their doctrine of Sentient Energy Fields (SEFs) and the Church's concern over "Soul Death" ?

Oh, a doctrine I cannot remember. Where is the SEF doctrine from?
Generally speaking, the benefits of Tech use vs. the dangers of corruption is a major point of content in the Universal Church. I often have the feeling that the individual sects, including the Urth Orthodoxy (which for all intents and purposes IS the Universal Church) are more lenient than the rules dictate. Practical exceptions are often rubber stamped. The Sanctuary Aeon's argument for prostetic cures to injuries is a strong one, and the Universal Church will probably not make too much of a fuzz about it if it's a noble or other VIP "privileged martyr" who benefits from the cybernetics.

As with all things, I think it boils down to local authority. If the local Bishop choses to make a fuzz, the cybernetics will be adressed. Alternatively, some Temple Avestite pressure group could lobby the Bishop to take not - "fix this abomination, your worshipfulness, our we'll picket your mass with howling flagelants for the next seven weeks."

I think the Sanctuary Aeon policy with cybernetics falls in line with the Privilege of Martyrs. If you are already taking on the burden of sin then replacing your body parts so you can continue your work is just a greater threshold of sin. Peasants however would not be given so much as a hook or pegleg for concern that it will rob them of what sacred energy the posess.
That said your noble will be given very grave warnings about the burden of cybernetics and the Amaltheans may insist you take a Sanctuary Aeon confessor to both maintain your cybernetics and your soul.

I like what has been said so far and think that it is very dependent on the situation calling for cybernetic replacement as well. I can see Amaltheans being OK with it when it is merely a cybernetic replacement of something lost (possibly defending the church?) but probably not so much for improving on the Pancreator's designs.